Rumen Metagenomics

Chapter

Abstract

The rumen microbiome plays a critical role in normal physiology and nutrition of ruminants. Alterations in the rumen microbiome have important physiological and pathological implications. The advent of next-generation sequencing technologies and rapid development of computational tools and reference databases provide powerful tools in rumen microbiome studies. Rumen metagenomics enables studies on the collective genetic structure and functional composition of the rumen microbial community in a culture-independent manner and can be simply divided into functional metagenomics and sequencing-based computational metagenomics. Recent progresses in mining the rumen microbial community for novel enzymes, such as fibrolytic enzymes, or other biomolecules for industry and biotechnology applications using functional screening are discussed. Rapid advances in computational metagenomic tools and methods are summarized. Metagenomics has provided novel insights into the structure and function of the rumen microbiome. Recent efforts suggest that the core rumen microbiome consists of 8 phyla and 15 families, which likely contribute to the basic function of the rumen. Systematic investigations of the rumen microbiome, including its viral (virome) and plasmid (plasmidome) fractions, have revealed previously unrecognized biodiversity in the rumen. Resistance and resilience of the rumen microbial community in response to perturbation is also discussed. Moreover, the need for mechanistic models and applications of general ecological theories and principles in rumen metagenomic studies is emphasized.

Keywords

Rumen Microbiome Microbiota, metagenomics 16S rRNA gene Functional screening Ruminant Microbial Ecosystem Resilience Next-generation sequencing Assembly 
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Notes

Acknowledgments

Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the US Department of Agriculture. The USDA is an equal opportunity provider and employer.

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Copyright information

© Springer India 2015

Authors and Affiliations

  1. 1.United States Department of Agriculture, Agriculture Research ServiceAnimal Genomics and Improvement LaboratoryBeltsvilleUSA

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